Tiger Woods had a poor day, though, and finished six off the pace on the course on the outskirts of Chicago.
Thomas said he had had a terrible warm up before the first round.
"I mean, I probably would say that I had the worst warm up I've ever had in my life this morning," he told reporters.
"I didn't know what it was going to do. I didn't know how I was going to hit it. My dad [caddie Jimmy Johnson] and I just kind of said that we were going to have to guess out there and just try to find something."
He ended the day with seven birdies, a joint course record and joint lead.
As well as Thomas and Kokrak, three other players have shot 65 at Medinah: Skip Kendall at the 1999 PGA Championship, and Mike Weir and winner Tiger Woods at the 2006 PGA.
Woods, who got two of his 15 major championship wins at Medinah, started well with three birdies in the first five holes.
He got one more birdie before the day was out, but also three bogeys.
"Didn't chip it, didn't make that many putts and consequently I'm one under," Woods told reporters.
"It's just not sharp, I'm trying to make changes in my swing and it's just not quite there yet.
"I need reps and I just haven't put in a lot of reps.
"I didn't feel any tightness in my oblique at all, I didn't feel any pull and so that was a positive, I just need to clean up my rounds and get going."
Englishman Justin Rose finished the day on four-under, with Northern Ireland's Rory McIlroy one further back on three-under 69.